angie: changes by commit

review to branch (2010-02-10 to 2010-02-16) v225

• kent/src/lib is 2, not 3 directory levels above.
  • src/hg/blastToPsl/makefile 1.30 - lines changed: 1, context: html, text, full: html, text
• Added cgiSpoof so the new cgiOptionalString in hgFind.c doesn't make cgiInit freak out.
  • src/hg/hgGetAnn/hgGetAnn.c 1.7 - lines changed: 2, context: html, text, full: html, text
• Removing - Chris says they are not needed here.
  • src/hg/visiGene/microscope.as 1.2 - lines changed: 60, context: html, text, full: html, text
  • src/hg/visiGene/microscope.sql 1.2 - lines changed: 88, context: html, text, full: html, text
• Fix: handle soft-clipping when fetching query sequence.
  • src/hg/hgTracks/bamTrack.c 1.25 - lines changed: 5, context: html, text, full: html, text
  • src/hg/hgc/bamClick.c 1.15 - lines changed: 8, context: html, text, full: html, text
  • src/hg/inc/bamFile.h 1.14 - lines changed: 6, context: html, text, full: html, text
  • src/hg/lib/bamFile.c 1.19 - lines changed: 38, context: html, text, full: html, text
• .o files should not be checked in.
  • src/hg/instinct/hgMicroscope/microscope/testMicroscopeSearch.o 1.2 - lines changed: 0, context: html, text, full: html, text
  • src/hg/instinct/hgMicroscope/microscopeLoad/exampleLoadingScript/vgLoadTest.o 1.2 - lines changed: 0, context: html, text, full: html, text
• In searchKnownCanonical, no need to include knownGene in the query because kgXref and knownCanonical can be joined directly - thanks for catching that Tim.
  • src/hg/lib/hgFind.c 1.225 - lines changed: 4, context: html, text, full: html, text
• Added printTrackUiLink in doBamDetails.
  • src/hg/hgc/bamClick.c 1.16 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgc/hgc.h 1.49 - lines changed: 3, context: html, text, full: html, text